LAMMPS (15 Apr 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
  using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

read_data tiny_nylon.data
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  44 atoms
  reading velocities ...
  44 velocities
  scanning bonds ...
  9 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  29 = max dihedrals/atom
  scanning impropers ...
  29 = max impropers/atom
  reading bonds ...
  42 bonds
  reading angles ...
  74 angles
  reading dihedrals ...
  100 dihedrals
  reading impropers ...
  44 impropers
  4 = max # of 1-2 neighbors
  6 = max # of 1-3 neighbors
  12 = max # of 1-4 neighbors
  41 = max # of special neighbors
  special bonds CPU = 0.000385045 secs
  read_data CPU = 0.013443 secs

variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2
variable prob2 equal (step/v_runsteps)>0.5

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule template mol1:
  1 molecules
  18 atoms with max type 8
  16 bonds with max type 14
  25 angles with max type 28
  23 dihedrals with max type 36
  14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule template mol2:
  1 molecules
  18 atoms with max type 9
  17 bonds with max type 13
  31 angles with max type 27
  39 dihedrals with max type 33
  20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule template mol3:
  1 molecules
  15 atoms with max type 9
  14 bonds with max type 13
  25 angles with max type 27
  30 dihedrals with max type 33
  16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule template mol4:
  1 molecules
  15 atoms with max type 11
  13 bonds with max type 15
  19 angles with max type 29
  16 dihedrals with max type 32
  10 impropers with max type 13

thermo 50

# dump 1 all xyz 1 test_vis.xyz

fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (src/USER-REACTION/fix_bond_react.cpp:2051)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp 300 300 100

# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]

# restart 100 restart1 restart2

run ${runsteps}
run 1000
PPPM initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:332)
  G vector (1/distance) = 0.0534597
  grid = 2 2 2
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0402256
  estimated relative force accuracy = 0.000121138
  using double precision FFTW3
  3d grid and FFT values/proc = 343 8
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 10 10 10
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
WARNING: Inconsistent image flags (src/domain.cpp:812)
Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes
Step Temp Press Density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2] 
       0          300    346.78165 0.0034851739            0            0            0            0 
      50    262.63913   -492.10749 0.0034851739          0.1            0            1            0 
     100    766.52962   -29.714349 0.0034851739          0.2            0            1            0 
     150    503.86837    50.220304 0.0034851739          0.3            0            1            0 
     200    456.51295    12.312892 0.0034851739          0.4            0            1            0 
     250    391.54928    9.2335844 0.0034851739          0.5            0            1            0 
     300     336.6988   -47.193937 0.0034851739          0.6            0            1            0 
     350    254.06985   -9.2867898 0.0034851739          0.7            0            1            0 
     400    259.41098   -25.657321 0.0034851739          0.8            0            1            0 
     450    258.10364      22.5086 0.0034851739          0.9            0            1            0 
     500    272.13412   -6.5391448 0.0034851739            1            0            1            0 
     550    202.75504    54.658731 0.0034851739          1.1            1            1            1 
     600    344.79887    23.798478 0.0034851739          1.2            1            1            1 
     650    328.44488   -29.908484 0.0034851739          1.3            1            1            1 
     700    280.13593   -8.3223255 0.0034851739          1.4            1            1            1 
     750    300.67624    1.0632669 0.0034851739          1.5            1            1            1 
     800    376.64234    12.488392 0.0034851739          1.6            1            1            1 
     850    321.07642    19.814074 0.0034851739          1.7            1            1            1 
     900    332.23751    30.814079 0.0034851739          1.8            1            1            1 
     950    311.14029    5.7853136 0.0034851739          1.9            1            1            1 
    1000    253.14634   -37.560642 0.0034851739            2            1            1            1 
Loop time of 0.379454 on 1 procs for 1000 steps with 44 atoms

Performance: 227.696 ns/day, 0.105 hours/ns, 2635.368 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.069723   | 0.069723   | 0.069723   |   0.0 | 18.37
Bond    | 0.14802    | 0.14802    | 0.14802    |   0.0 | 39.01
Kspace  | 0.044252   | 0.044252   | 0.044252   |   0.0 | 11.66
Neigh   | 0.072359   | 0.072359   | 0.072359   |   0.0 | 19.07
Comm    | 0.0044748  | 0.0044748  | 0.0044748  |   0.0 |  1.18
Output  | 0.0022775  | 0.0022775  | 0.0022775  |   0.0 |  0.60
Modify  | 0.036509   | 0.036509   | 0.036509   |   0.0 |  9.62
Other   |            | 0.00184    |            |       |  0.48

Nlocal:    44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    722 ave 722 max 722 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 722
Ave neighs/atom = 16.4091
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:00
